Neisseria meningitidis (NM) serogroup B has been the predominant meningococcal serogroup in Brazil, but no broadly effective vaccine is available. To better understand genetic diversity among serogroup B strains in Brazil, we selected a nationally representative sample of clinical disease isolates from 2004, and a temporally representative sample of disease isolates for the state of So Paulo (1988 2006) for further study (n=372). We performed multi-locus sequence typing (MLST) and sequence analysis of five outer membrane protein (OMP) genes, including novel vaccine targets fHbp and nadA. In 2004, strain B: 4;P1.15,19 clonal complex ST-32 /ET-5 (cc32) predominated throughout Brazil. Among strains of this type, we identified significant regional variation in MLST sequence type (ST), fetA, and porB but limited diversity in nadA and fHbp. Between 1988 and 1996, the SP isolates shifted from clonal complex ST-41/44 complex/Lineage 3 (cc41/44) to cc32. cc41/44 strains had significantly greater diversity in ST relative to cc32 strains;OMP variation was associated with but not predicted by cc or ST. All fHbp sequences were variant 1/subfamily B and the majority of nadA, were similar to allele 1. A predominant serogroup B lineage has circulated in Brazil for over a decade with significant regional and temporal diversity developing in ST, fetA, and porB, but not for OMP genes nadA and fHbp.